The treatment-naive microbiome in new-onset Crohn's disease

Dirk Gevers, Subra Kugathasan, Lee A. Denson, Yoshiki Vázquez-Baeza, Will Van Treuren, Boyu Ren, Emma Schwager, Dan Knights, Se Jin Song, Moran Yassour, Xochitl C. Morgan, Aleksandar D. Kostic, Chengwei Luo, Antonio González, Daniel McDonald, Yael Haberman, Thomas Walters, Susan Baker, Joel Rosh, Michael Stephens & 12 others Melvin Heyman, James Markowitz, Robert Baldassano, Anne Griffiths, Francisco Sylvester, David Mack, Sandra Kim, Wallace Crandall, Jeffrey Hyams, Curtis Huttenhower, Rob Knight, Ramnik J. Xavier

Research output: Contribution to journalArticle

968 Citations (Scopus)

Abstract

Inflammatory bowel diseases (IBDs), including Crohn's disease (CD), are genetically linked to host pathways that implicate an underlying role for aberrant immune responses to intestinal microbiota. However, patterns of gut microbiome dysbiosis in IBD patients are inconsistent among published studies. Using samples from multiple gastrointestinal locations collected prior to treatment in new-onset cases, we studied the microbiome in the largest pediatric CD cohort to date. An axis defined by an increased abundance in bacteria which include Enterobacteriaceae, Pasteurellacaea, Veillonellaceae, and Fusobacteriaceae, and decreased abundance in Erysipelotrichales, Bacteroidales, and Clostridiales, correlates strongly with disease status. Microbiome comparison between CD patients with and without antibiotic exposure indicates that antibiotic use amplifies the microbial dysbiosis associated with CD. Comparing the microbial signatures between the ileum, the rectum, and fecal samples indicates that at this early stage of disease, assessing the rectal mucosal-associated microbiome offers unique potential for convenient and early diagnosis of CD.

Original languageEnglish (US)
Pages (from-to)382-392
Number of pages11
JournalCell Host and Microbe
Volume15
Issue number3
DOIs
StatePublished - Mar 12 2014
Externally publishedYes

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Microbiota
Crohn Disease
Dysbiosis
Inflammatory Bowel Diseases
Veillonellaceae
Rectal Diseases
Anti-Bacterial Agents
Enterobacteriaceae
Therapeutics
Ileum
Rectum
Early Diagnosis
Bacteria
Gastrointestinal Microbiome

All Science Journal Classification (ASJC) codes

  • Parasitology
  • Microbiology
  • Virology

Cite this

Gevers, D., Kugathasan, S., Denson, L. A., Vázquez-Baeza, Y., Van Treuren, W., Ren, B., ... Xavier, R. J. (2014). The treatment-naive microbiome in new-onset Crohn's disease. Cell Host and Microbe, 15(3), 382-392. https://doi.org/10.1016/j.chom.2014.02.005
Gevers, Dirk ; Kugathasan, Subra ; Denson, Lee A. ; Vázquez-Baeza, Yoshiki ; Van Treuren, Will ; Ren, Boyu ; Schwager, Emma ; Knights, Dan ; Song, Se Jin ; Yassour, Moran ; Morgan, Xochitl C. ; Kostic, Aleksandar D. ; Luo, Chengwei ; González, Antonio ; McDonald, Daniel ; Haberman, Yael ; Walters, Thomas ; Baker, Susan ; Rosh, Joel ; Stephens, Michael ; Heyman, Melvin ; Markowitz, James ; Baldassano, Robert ; Griffiths, Anne ; Sylvester, Francisco ; Mack, David ; Kim, Sandra ; Crandall, Wallace ; Hyams, Jeffrey ; Huttenhower, Curtis ; Knight, Rob ; Xavier, Ramnik J. / The treatment-naive microbiome in new-onset Crohn's disease. In: Cell Host and Microbe. 2014 ; Vol. 15, No. 3. pp. 382-392.
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abstract = "Inflammatory bowel diseases (IBDs), including Crohn's disease (CD), are genetically linked to host pathways that implicate an underlying role for aberrant immune responses to intestinal microbiota. However, patterns of gut microbiome dysbiosis in IBD patients are inconsistent among published studies. Using samples from multiple gastrointestinal locations collected prior to treatment in new-onset cases, we studied the microbiome in the largest pediatric CD cohort to date. An axis defined by an increased abundance in bacteria which include Enterobacteriaceae, Pasteurellacaea, Veillonellaceae, and Fusobacteriaceae, and decreased abundance in Erysipelotrichales, Bacteroidales, and Clostridiales, correlates strongly with disease status. Microbiome comparison between CD patients with and without antibiotic exposure indicates that antibiotic use amplifies the microbial dysbiosis associated with CD. Comparing the microbial signatures between the ileum, the rectum, and fecal samples indicates that at this early stage of disease, assessing the rectal mucosal-associated microbiome offers unique potential for convenient and early diagnosis of CD.",
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Gevers, D, Kugathasan, S, Denson, LA, Vázquez-Baeza, Y, Van Treuren, W, Ren, B, Schwager, E, Knights, D, Song, SJ, Yassour, M, Morgan, XC, Kostic, AD, Luo, C, González, A, McDonald, D, Haberman, Y, Walters, T, Baker, S, Rosh, J, Stephens, M, Heyman, M, Markowitz, J, Baldassano, R, Griffiths, A, Sylvester, F, Mack, D, Kim, S, Crandall, W, Hyams, J, Huttenhower, C, Knight, R & Xavier, RJ 2014, 'The treatment-naive microbiome in new-onset Crohn's disease', Cell Host and Microbe, vol. 15, no. 3, pp. 382-392. https://doi.org/10.1016/j.chom.2014.02.005

The treatment-naive microbiome in new-onset Crohn's disease. / Gevers, Dirk; Kugathasan, Subra; Denson, Lee A.; Vázquez-Baeza, Yoshiki; Van Treuren, Will; Ren, Boyu; Schwager, Emma; Knights, Dan; Song, Se Jin; Yassour, Moran; Morgan, Xochitl C.; Kostic, Aleksandar D.; Luo, Chengwei; González, Antonio; McDonald, Daniel; Haberman, Yael; Walters, Thomas; Baker, Susan; Rosh, Joel; Stephens, Michael; Heyman, Melvin; Markowitz, James; Baldassano, Robert; Griffiths, Anne; Sylvester, Francisco; Mack, David; Kim, Sandra; Crandall, Wallace; Hyams, Jeffrey; Huttenhower, Curtis; Knight, Rob; Xavier, Ramnik J.

In: Cell Host and Microbe, Vol. 15, No. 3, 12.03.2014, p. 382-392.

Research output: Contribution to journalArticle

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AU - Kugathasan, Subra

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AU - Sylvester, Francisco

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AU - Kim, Sandra

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AU - Hyams, Jeffrey

AU - Huttenhower, Curtis

AU - Knight, Rob

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Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host and Microbe. 2014 Mar 12;15(3):382-392. https://doi.org/10.1016/j.chom.2014.02.005